Genetic testing has been available in the domestic cat since the 1960s, but as like other species, over the past 50 years, the level of resolution has improved from the chromosome level to the sequence level. Knowing the direct causative mutation for a trait or disease assists cat breeders with the breeding programs and can help clinicians determine heritable presentations versus idiopathic versions of a health concern. Genetic tests cover all the various forms of DNA variants, including chromosomal abnormalities, mtDNA variation, gene loss, translocations, large inversions, small insertions and deletions and the simple nucleotide substitutions. Higher throughput technologies have made genetic testing cheaper, simpler, and faster, thereby making cat genetic testing affordable to the lay public and small animal practice clinicians. The genetic resources for cats and other animal species have also opened the doors for animal evidence to be supportive in criminal investigations. This presentation will highlight the various tests available for the domestic cat and their specific capabilities and roles in cat health and management.

Cat Chromosomes

Some of the earliest genetic testing for any species was the examination of the chromosomes to determine the presence of the normal and complete genomic complement. Early studies of mitotic chromosomes of the domestic cat revealed an easily distinguishable karyotype consisting of 18 autosomal chromosomes and the XY sex chromosome pair, resulting in a 2N complement of 38 chromosomes for the cat genome.1 Sex chromosome aneuploidies and trisomies of small acrocentric chromosomes were typically associated with cases of decreased fertility and syndromes that displayed distinct morphological presentations. Turner's Syndrome (XO), Klinefelter's Syndrome (XXY) and chimerism have been documented in the domestic cat. Because cat has a highly recognizable X-linked trait,2-5Orange, and the X-inactivation process was recognized,6 tortoiseshell and calico male cats were the first feline suspects of chromosomal abnormalities. Karyotypic and now gene-based assays are common methods to determine if a cat with ambiguous genitalia7 or a poor reproductive history has a chromosomal abnormality. Karyotypic studies of male tortoiseshell cats have shown that they are often mosaics, or chimeras, being XX/XY in all or some tissues.5,8-15 The minor chromosomal differences that are cytogenetically detectable between a domestic cat and an Asian leopard cat are likely the cause of fertility problems in the Bengal cat breed, which is a hybrid between these two species.16 Other significant chromosomal abnormalities causing common "syndromes" are not well documented in the cat. Several research and commercial laboratories can perform cat chromosomal analyses when provided a living tissue, such as a fibroblast biopsy or whole blood for the analysis of white blood cells.

Inherited Disease Tests

The candidate gene approach has been fruitful in domestic cat investigations for the identification of many diseases and trait mutations. The first mutations identified were for a gangliosidosis and muscular dystrophy, discovered in the early and mid-1990s,17,18 as these diseases have well-defined phenotypes and known genes with mutations that were found in humans. Most of the common diseases, coat colors, and coat types were deciphered in the cat following the same candidate gene approach.

Most of the identified disease tests in cats that are very specific to breeds and populations are available as commercial genetic tests (Table 1). Typically, diseases are identified in cat breeds, which are a small percentage of the cat population of the world, perhaps at most 10–15% in the USA.19 However, some mutations that were found in a specific breed, such as mucopolysaccharidosis in the Siamese,20,21 were found in a specific individual, and the mutation is not of significant prevalence in the breed (Table 2). These genetic mutations should not be part of routine screening by cat breeders and registries, but clinicians should know that genetic tests are available for diagnostic purposes, especially from research groups with specialized expertise, such as at the University of Pennsylvania (http://research.vet.upenn.edu/penngen). Other diseases, such as polycystic kidney disease (PKD), are prevalent; PKD in Persians is estimated at 30–38% worldwide.22-24 Because of cross-breeding with Persians, many other breeds - such as British Shorthairs, American Shorthairs, Selkirk Rex, and Scottish Folds - also need to be screened for PKD.25-27 As PKD testing begins to become less common, as breeders remove positive cats, other genetic tests are becoming more popular, such as coat color and other disease traits (Figure 1).

Table 1. Common commercialized DNA tests for domestic cats

Disease/trait (alleles)

MOI*

Phenotype

Breeds

Gene

Mutation

Agouti (A+, a)36

AR

Banded fur to solid

All cats

ASIP

c.122_123delCA

Amber (E+, e)37

AR

Brown color variant

Norwegian Forest

MC1R

c.250G>A

Brown (B+, b, bl)38,39

AR

Brown, light brown color variants

All cats

TYRP1

b = c.8C>G, bl = c.298C>T

Color (C+, Cb, Cs, c)39-41

AR

Burmese, Siamese color pattern, full albino

All breeds

TYR

cb = c.715G>T, cs = c.940G>A, c = c.975delC

Dilution (D+, d)42

AR

Black to grey/blue
Orange to cream

All cats

MLPH

c.83delT

Extension (E+, e) - Amber37

AR

Brown/red color variant

Norwegian Forest

MC1R

c.250G>A

Fold (Fd, fd+)

AD

Ventral ear fold

Scottish Fold

In press

Gloves (G+, g)43

AR

White feet

Birman

KIT

In press

Hairless (Hr+, hr)44

AR

Atrichia

Sphynx

KRT71

c.816+1G>A

Inhibitor

AD

Absence of phaeomelanin

All cats

Long fur (L+, l)45,46

AR

Long fur

All cats**

FGF5

c.356_367insT, c.406C>T, c.474delT, c.475A>C

Manx (M, m+)

AD

Absence/short tail

Manx, American Bobtail, PixieBob

c.998delT, c.1169delC, and c.1199delC, c.998_1014dup17delGCC

Rexing (R+, r)47

AR

Curly hair coat

Cornish Rex

PYP2R5

c.250_253delTTTG

Rexing (Re+, re)44

AR

Curly hair coat

Devon Rex

KRT71

c.1108-4_1184del, c.1184_1185insAGTTGGAG, c.1196insT

Rexing48

AD

Curly hair coat

Selkirk Rex

KRT71

c.445-1G>C

Tabby49

AR

Blotched/classic pattern

All cats

TAQPEP

S59X, T139N, D228N, W841X

AB blood type (A+, b)50

AR

Determines type B

All cats

CMAH

c.1del-53_70, c.139G>A

Craniofacial defect

AR

Craniofacial defect

Burmese

In press

Gangliosidosis 151

AR

Lipid storage disorder

Korat, Siamese

GBL1

c.1457G>C

Gangliosidosis 252

AR

Lipid storage disorder

Burmese

HEXB

c.1356del-1_8, c.1356_1362delGTTCTCA

Gangliosidosis 218

AR

Lipid storage disorder

Korat

HEXB

c.39delC

Glycogen storage dis. IV53

AR

Glycogen storage disorder

Norwegian Forest

GBE1

IVS11+1552_IVS12-1339 del6.2kb ins334 bp

Hypertrophic cardiomyopathy32

AD

Cardiac disease

Maine Coon

MYBPC

c.93G>C

Hypertrophic cardiomyopathy54

AD

Cardiac disease

Ragdoll

MYBPC

c.2460C>T

Hypokalemia55

AR

Potassium deficiency

Burmese

WNK4

c.2899C>T

Progressive retinal atropy56

AR

Late-onset blindness

Abyssinian

CEP290

IVS50 + 9T>G

Progressive retinal atropy57

AD

Early-onset blindness

Abyssinian

CRX

c.546delC

Polycystic kidney disease27

AD

Kidney cysts

Persian

PKD1

c.10063C>A

Pyruvate kinase def.58

AR

Hemopathy

Abyssinian

PKLR

c.693+304G>A

Spinal muscular atrophy59

AR

Muscular atrophy

Maine Coon

LIX1-LNPEP

Partial gene deletions

* Mode of inheritance of the non-wild-type variant
** Long fur variants are more or less common depending on the breed. Not all transcripts for a given gene may have been discovered or well documented in the cat; mutations presented as interpreted from original publication.

Table 2. Other mutations for inherited domestic cat diseases*

Disease

Gene

Mutation**

Disease

Gene

Mutation**

11b-hydroxylase
def. (congenital adrenal hypoplasia)60

CYP11B1

Exon 7 G>A

Mucopolysaccharidosis I61

IDUA

c. 1107_1109delCGA or c. 1108_1110 GAC

Dihydropyrimidinase Def.

DPY8

c.1303G>A

Mucopolysaccharidosis VI21

ARSB

c.1427T>C

Fibrodysplasia ossificans progressiva

ACVR1

G617A (R206H)

Mucopolysaccharidosis VI20,62

ARSB

c.1558G>A

Gangliosidosis 163

GLB1

c.1448G>C

Gangliosidosis 264

HEXB

c.1467_1491inv

Mucopolysaccharidosis VII65

GUSB

c.1052A>G

Gangliosidosis 266

HEXB

c.667C>T

Niemann-Pick C67

NPC

c.2864G>C

Gangliosidosis 253

GM2A

c.390_393GGTC

Polydactyla68

SHH

c.479A>G

Hemophilia B69

F9

c.247G>A

Polydactyla68

SHH

c.257G>C, c.481A>T

Hemophilia B69

F9

c.1014C>T

Porphyria (congenital erythropoietic)70

UROS

c.140C>T, c.331G>A

Hyperoxaluria71

GRHPR

G>A I4 acceptor site

Porphyria (acute intermittent)72

HMBS

c.842_844delGAG, c.189dupT, c.250G>A, c.445C>T

Lipoprotein lipase def.73

LPL

c.1234G>A

Vitamin D-resistant rickets74

CYP27B1

c.223G>A, c.731delG

Mannosidosis, alpha75

LAMAN

c.1748_1751delCCAG

Vitamin D-resistant rickets76

CYP27B1

c.637G>T

Mucolipidosis II77

GNPTA

c.2655C>T

* The presented conditions are not prevalent in breeds or populations but may have been established into research colonies.
** Not all transcripts for a given gene may have been discovered or well documented in the cat; mutations presented as interpreted from original publication.

Figure 1. Trends of genetic testing in the domestic cat

DNA-based genetic tests are presented for the cat. Parentage and individual identification (DNA) has not increased, as cats do not require testing for registration. One of the most popular tests, PKD, is presented separately to show that the testing requests are decreasing as breeders are eliminating positive cats from breeding programs. Other disease tests and color tests are becoming more popular tests in the cat market.

Genetic Testing Concerns in Hybrid Cat Breeds

Several cat breeds were formed by crossing with different species of cats. The Bengal breed is acknowledged worldwide and has become a highly popular breed. To create Bengals, Asian leopard cats (Felis bengalensis) were and are bred with domestic cat breeds like Egyptian Mau, Abyssinian and other cats to form a very unique breed in both color and temperament.28 An Asian leopard cat had a common ancestor with the domestic cat about 6 million years ago, the bobcat about 8 million years ago, the Serval about 9.5 million years ago.29 The Jungle cat is more closely related to a domestic cat than the leopard cat to the domestic cat. In addition, for some of these wild felid species, different subspecies were incorporated into the breed. The DNA sequence between a domestic cat and one of these wild felid species will have many genetic differences, less for the Jungle cat, more for Serval as compared to a domestic cat. The genetic differences are most likely silent mutations, but the variation will interplay with genetic assays and may cause more allelic dropout than what would be normally anticipated. No genetic tests are validated in the hybrid cat breeds, although the tests are typically used very frequently in Bengal cats. Thus, the accuracy for any genetic test is not known for hybrid cat breeds. A genetic test for the charcoal coloration in Bengals will likely soon be available and is unique due to the hybridization with leopard cats.

Race and Breed Identification

A newly developing test for the domestic cat is a race and breed identification panel. Based on the studies by Lipinski et al. (2008)30 and Kurushima et al. (2012, submitted), STRs have been tested in a variety of random-bred cats from around the world and a majority of the major cat breeds of the USA and other regions. The genetic studies have been able to differentiate eight worldwide populations of cats - races - and can distinguish the major breeds. Analyses of the present-day random-bred cat populations suggest that the regional populations are highly genetically distinct, hence analogous to humans, different races of cats. The regional genetic differentiation is captured and displayed within the breeds that developed later from those populations. The foundation population (race) of the Asian breeds, such as Burmese and Siamese, is comprised of the street cats of Southeast Asia, whereas the foundation population (race) of the Maine Coon and Norwegian Forest cat is comprised of Western European cats. Phenotypic markers help to delineate breeds within specific breed families, such as the Persian, Burmese, and Siamese families. The cat race and breed identification tests are similar to tests that have been developed for the dog, such as the Mars, Inc. Wisdom Panel (www.wisdompanel.com). Although similar, domestic cats are random-bred cats and not a concoction of pedigreed breed cats. Cat breeds developed from the random-bred populations that have existed in different regions of the world for thousands of years. Therefore, the claims of the cat race and breed identification tests are different than the dog tests, not claiming that most household cats are recent offspring of pedigreed cats.

Implications for Cat Health & Breeding

To date, most cat genetic tests have been for traits that have nearly complete penetrance, having little variability in expression, and early onset. These aspects are important when considering management in the breed. If your cat has the PKD mutation, it will get kidney cysts, but the development of renal failure is variable (variable expression). Therefore, some recognized mutations in cats might be considered risk factors, predisposing an individual to health problems. Excellent examples of mutations that confer a risk in cats are the DNA variants associated with cardiac disease in cats. Hypertrophic cardiomyopathy (HCM) is a recognized genetic condition.31 In 2005, Drs. Meurs, Kittleson and colleagues published that a DNA alteration, A31P, in the gene cardiac myosin-binding protein C 3 (MYBPC3) was strongly associated with HCM in a long-term research colony of Maine Coon cats at UC Davis.32 Recent studies have shown that not all Maine Coon cats with the A31P mutation get HCM,33,34 and one of those papers has mistakenly interpreted this lack of penetrance as being evidence that the A31P mutation is not causal34. This interpretation is misleading, causing debate as to the validity of the Maine Coon HCM test. As true in humans with cardiac disease, the finding that not all cats with the A31P mutation in MYBPC3 get HCM is actually usual in the field of HCM genetic testing.

Like cat HCM mutations, other disease mutations have shown variation in penetrance and expression, such as the CEP290 PRA mutation in Abyssinians, and some cats with the pyruvate kinase deficiency can have very mild and subclinical presentations.35 Thus, disease or trait causing mutations may not be 100% penetrant; thus, they do not always cause clinically detectable disease.

Conclusion

Many aspects of the population and the specific mutation must be considered during management of a disease. Diseases with a low frequency in a large population could likely be eliminated. Diseases in a very high frequency or present in a very small population need to be slowly removed from the population with great care. Genetic testing is an important diagnostic tool for the veterinarian, breeder, and owner. Genetic tests are not 100% foolproof, and the accuracy of the test procedure and the reputation and customer service of the genetic testing laboratory need to be considered. Some traits are highly desired, and genetic testing can help breeders to more accurately determine appropriate breedings, potentially becoming more efficient breeders, thus lowering costs and excess cat production. Other traits or diseases are undesired, thus genetic testing can be used to prevent disease, potentially eradicating the concern from the population. Genetic tests for simple genetic traits are more consistent with predicting the trait or disease presentation, but, as genomics progress for the cat, more tests that confer risk will become more common.

Figure 2. The slippery slope of mutation lethality

Some mutations are so severe, they cause death in utero, such as PKD and taillessness. Some have high and severe penetrance, while others have low and mild penetrance. All these factors and others should be considered when managing a cat population.